I calculated GROMACS Energy of a protein molecule using "gmx energy -f md.edr" command. I got Potential Energy, Kinetic Energy, Total Energy, Pressure, Volume, Density, Enthalpy, and Surface Tension at 320 K. When I increase the temperature to 340 K, These energy changes. Like Pressure decreases, and components such as Volume, Enthalpy, and surface tension increases. Is it just because increase in temperature leads to increase in volume? Does this calculation has some significant meaning. I think its nothing related to Protein molecule. Please suggest.
You heated the system, so it expanded. Simple thermodynamics. The better question is - what do you hope to learn about your system by calculating those quantities? None will tell you anything useful about the protein.
Dear Faez,
Gmx_energy extracts energy components from an energy file. Gromacs write an .edr file with energy values (in fact, it store energies, temperature, pressure, box size, density etc), which you are passing as an input for gmx_energy command. Basically, gromacs dump these calculated variables, which depends on upon the initial temperature and velocity of the systems, into an energy (md.edr) file. So if you are increasing the temperature, it's normal to see the changes in the values, as per the law of thermodynamics.
It might help you to detect any strange behaviour in your system, say energy spikes suddenly.
It's kinda hard to say anything since you didn't really say what kind of simulation you were running (NVT, NVE, NPT) or what it is you were trying to achieve. In any case, you're heating up the system so by definition the kinetic energy will be higher and as a consequence the potential energy will also increase. The total energy being the sum of the two will also increase.
If you do the DFT or FFT of the energy trajectory and if there are oscillations then you can get that information.
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